Analysis of the algorithm: From embeddings to prioritized genes.

The algorithm transformed the similarity matrix to make it compatible with the embedding process. Once this was done for each network and embedding type, it was integrated by embedding type. Below there is a general analysis of the properties of each matrix in the different phases of the process, including the graph building process for each layer.

Annotations Properties

Table 1. Annotation descriptors.

Net Min Max Average Standard_Deviation
DepMap_effect 972 17354 2043.6562906724512 3829.1218209282715
biological_process 1 1053 8.255678448065316 20.730757162592834
cellular_component 1 5172 7.219656420451649 82.56741928666138
disease 1 81 1.7829472267615112 2.3512948371338793
gene_PS 1 108 2.1519058295964126 5.045578888786698
gene_TF 1 5778 3.0320060963993143 74.46796191948712
gene_hgncGroup 1 2294 2.261042369703787 23.27548667222241
hippie_ppi 1 2985 84.68724915097252 150.1286010250888
molecular_function 1 6791 4.87167748867193 54.08093332133869
pathway 1 479 6.75436035343834 16.179001796162975
phenotype 1 1307 23.941396322320227 48.71098651648341
string_ppi 1 7338 610.0699285559645 500.6662722348227

Individual Processing Graph steps

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Embedding Process

Table 2. Uncombined Embedding Matrixes

Net Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
DepMap_effect_pearson ct 17354x17354 301161316 301161316 1.0
DepMap_effect_pearson el 17354x17354 301161316 301161316 1.0
DepMap_effect_pearson ka 17354x17354 301161316 106778670 0.35455639329189276
DepMap_effect_pearson raw_sim 17354x17354 301161316 106761316 0.35449876968926514
DepMap_effect_pearson rf 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman ct 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman el 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman ka 17354x17354 301161316 194719108 0.6465608219084817
DepMap_effect_spearman raw_sim 17354x17354 301161316 194701754 0.6465031983058541
DepMap_effect_spearman rf 17354x17354 301161316 301161316 1.0
biological_process ct 15641x15641 244640881 244640881 1.0
biological_process el 15641x15641 244640881 244640881 1.0
biological_process ka 15641x15641 244640881 213684707 0.8734627921814915
biological_process raw_sim 15641x15641 244640881 213680626 0.8734461105868891
biological_process rf 15641x15641 244640881 244640881 1.0
cellular_component ct 199x199 39601 39601 1.0
cellular_component el 199x199 39601 39601 1.0
cellular_component ka 199x199 39601 37757 0.9534355193050681
cellular_component node2vec 199x199 39601 39601 1.0
cellular_component raw_sim 199x199 39601 37614 0.9498244993813287
cellular_component rf 199x199 39601 39601 1.0
disease ct 4162x4162 17322244 17322244 1.0
disease el 4162x4162 17322244 17322244 1.0
disease ka 4162x4162 17322244 17230892 0.9947263183684516
disease raw_sim 4162x4162 17322244 17228280 0.9945755295907389
disease rf 4162x4162 17322244 17322244 1.0
gene_PS ct 362x362 131044 112096 0.8554073440981655
gene_PS el 362x362 131044 7680 0.05860626964988859
gene_PS ka 362x362 131044 2028 0.015475718079423705
gene_PS node2vec 362x362 131044 131044 1.0
gene_PS raw_sim 362x362 131044 1666 0.012713287140197186
gene_PS rf 362x362 131044 7680 0.05860626964988859
gene_TF ct 3871x3871 14984641 14984637 0.9999997330600046
gene_TF el 3871x3871 14984641 14969165 0.9989672091576969
gene_TF ka 3871x3871 14984641 5275373 0.35205201112258877
gene_TF raw_sim 3871x3871 14984641 5271502 0.35179367994201527
gene_TF rf 3871x3871 14984641 14969165 0.9989672091576969
gene_hgncGroup ct 25136x25136 631818496 631304330 0.9991862124909999
gene_hgncGroup el 25136x25136 631818496 326932198 0.5174463870079549
gene_hgncGroup ka 25136x25136 631818496 14482790 0.022922390040319426
gene_hgncGroup raw_sim 25136x25136 631818496 14457654 0.022882606462980154
gene_hgncGroup rf 25136x25136 631818496 326932198 0.5174463870079549
hippie_ppi ct 15763x15763 248472169 248472169 1.0
hippie_ppi el 15763x15763 248472169 245768483 0.9891187571997249
hippie_ppi ka 15763x15763 248472169 421467 0.0016962342370022132
hippie_ppi node2vec 15763x15763 248472169 248472169 1.0
hippie_ppi raw_sim 15763x15763 248472169 408340 0.0016434033704595704
hippie_ppi rf 15763x15763 248472169 245768483 0.9891187571997249
molecular_function ct 8072x8072 65157184 65157184 1.0
molecular_function el 8072x8072 65157184 65157184 1.0
molecular_function ka 8072x8072 65157184 65145888 0.9998266346194458
molecular_function raw_sim 8072x8072 65157184 65144771 0.9998094914599133
molecular_function rf 8072x8072 65157184 65157184 1.0
pathway ct 5611x5611 31483321 31482925 0.9999874219114305
pathway el 5611x5611 31483321 25851467 0.8211162666098663
pathway ka 5611x5611 31483321 362997 0.011529819233491919
pathway node2vec 5611x5611 31483321 31483321 1.0
pathway raw_sim 5611x5611 31483321 357386 0.011351597882574078
pathway rf 5611x5611 31483321 25851467 0.8211162666098663
phenotype ct 4486x4486 20124196 20124196 1.0
phenotype el 4486x4486 20124196 20124196 1.0
phenotype ka 4486x4486 20124196 20050882 0.996356922780915
phenotype raw_sim 4486x4486 20124196 20049900 0.9963081258004046
phenotype rf 4486x4486 20124196 20124196 1.0
string_ppi ct 16111x16111 259564321 259564321 1.0
string_ppi el 16111x16111 259564321 252333871 0.9721438987756719
string_ppi ka 16111x16111 259564321 497009 0.0019147816544478006
string_ppi node2vec 16111x16111 259564321 259564321 1.0
string_ppi raw_sim 16111x16111 259564321 480917 0.001852785460448549
string_ppi rf 16111x16111 259564321 252333871 0.9721438987756719

Table 3. Integrated Embedding Matrixes

Integration Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
integration_mean_by_presence ct 30121x30121 907274641 795014985 0.8762671732164065
integration_mean_by_presence el 30121x30121 907274641 568056685 0.6261132619929581
integration_mean_by_presence ka 30121x30121 907274641 289392049 0.3189685194783263
integration_mean_by_presence node2vec 18159x18159 329749281 315719059 0.9574518496069139
integration_mean_by_presence raw_sim 30121x30121 907274641 289376677 0.31895157642789224
integration_mean_by_presence rf 30121x30121 907274641 568056685 0.6261132619929581
mean ct 30121x30121 907274641 795014985 0.8762671732164065
mean el 30121x30121 907274641 568056685 0.6261132619929581
mean ka 30121x30121 907274641 289392049 0.3189685194783263
mean node2vec 18159x18159 329749281 315719059 0.9574518496069139
mean raw_sim 30121x30121 907274641 289376677 0.31895157642789224
mean rf 30121x30121 907274641 568056685 0.6261132619929581

Weight values